add prostate atlas

Author: myushen

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: CuratedAtlasQueryR
 Title: Queries the Human Cell Atlas
-Version: 1.3.7
+Version: 1.4.7
 Authors@R: c(
     person(
         "Stefano",
@@ -126,7 +126,7 @@ biocViews:
     Transcription,
     Transcriptomics
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/CuratedAtlasQueryR
 BugReports: https://github.com/stemangiola/CuratedAtlasQueryR/issues

R/metadata.R

@@ -10,7 +10,8 @@ cache <- rlang::env(
 )
 
 #' Returns the URLs for all metadata files 
-#' @param databases A character vector specifying the names of the metadata files. Default is c("metadata.0.2.3.parquet", "fibrosis.0.2.3.parquet")
+#' @param databases A character vector specifying the names of the metadata files. 
+#' Default is c("metadata.0.2.3.parquet", "fibrosis.0.2.3.parquet", "prostate.0.1.0.parquet")
 #' @export
 #' @return A character vector of URLs to parquet files to download
 #' @examples
@@ -20,7 +21,8 @@ cache <- rlang::env(
 #'   immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06.
 #'   doi:10.1101/2023.06.08.542671.
 #' @source [Mangiola et al.,2023](https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3)
-get_database_url <- function(databases = c("metadata.0.2.3.parquet", "fibrosis.0.2.3.parquet")) {
+get_database_url <- function(databases = c("metadata.0.2.3.parquet", "fibrosis.0.2.3.parquet",
+                                           "prostate.0.1.0.parquet")) {
   glue::glue(
     "https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/metadata/{databases}")
 }

man/get_database_url.Rd

@@ -253,4 +253,16 @@ test_that("get_pseudobulk() syncs appropriate fixed file", {
     expect_gt(1)
 })
 
+test_that("get_single_cell_experiment() syncs prostate atlas", {
+  temp <- tempfile()
+  # A sample from prostate atlas
+  sample <- "GSM4089151"
+  meta <- get_metadata(cache_directory = temp) |> filter(sample_ == sample)
+  sce <- meta |> get_single_cell_experiment(cache_directory = temp)
+  sce |>
+    row.names() |>
+    length() |>
+    expect_gt(1)
+})
+